To be fair, the only way we're likely to see an end of this is to see a removal, or serious reduction, of left wing influances from the US goverment, and perhaps the media as well.
Now, before anyone gets their panties in a bunch over me saying this (I know the audience) understand that one of the big problems with the media right now is that you can't have anyone as the bad guys. If you have Muslims, Blacks, Latinos, Chinese, or any other group largely making up the bad guys in the form of gang bangers, terrorists, foreign spies, criminal syndicates, or whatever else, your opening the door for people of that sort to jump in about the characterization of their nation, or the perpetuation of racial stereotypes, which the goverment and media proceeds to take seriously, and create a huge headache for the gaming industry as a whole. Left wing reviewers and critics do not help matters much.
I point towards say the last, and worst, Indiana Jones movie where the Russians got all pissed over being the bad guys in that movie, not to mention the outcries we saw over "The Sopranos" from various Italian-American groups. On a purely video game front look at what happened with "Resident Evil 5" and the whole reaction of "OMG, how dare you show African tribals as African tribals outside of National Geographic".
The point here is that Zombies are one of the very few things you can put into a game to rack up a body count, and dispose of with relative imputiny, that isn't going to cause a degree of backlash from the media, and politicians looking to get some attention (which is partially what fuels the media).
Now, don't get me wrong, both "wings" have their problems, and while there is some overlap the right wing mostly goes after sex and violence in general, while the left wing goes after games for being the boogie-man for not being politically correct. Both ruin our fun. In the end the right wing does tend to be more reasonable because the religious and moral crackpots are pretty well balanced by the business interests in the party who want to make a product that can sell, and as a whole it's a lot easier to rationalize with (certain individuals excepted) than a group of people that tie it into much biggier issues and want to do things like remove the freedom of speech to ban "hate speech" which by association would apply towards video games.
Right now we've pretty much got a triumverate of "acceptable" video games enemies... monsters, zombies, and aliens, which get recycled endlessly. Yahtzee's joking is not the only source that has accused "Uncharted" as a series of being racist for having a white protaganist fighting foreigners while hunting for/stealing treasure in foreign lands, and really it's one of the few games that still bucks the trend other than sandbox crime games. I personally suspect that the most recent work of the genere... "Saints Row 3" got away from any pretensions of realism and seriousness (unlike the last two) in order to hide from criticism behind the sheer insanity of the entire thing. The jury is still out on the new "Grand Theft Auto" but it seems to have gone in a differant, but similar, direction in terms of creating sympathetic characters and situations and trying to treat the subject matter with a degree of sensitivity, at least within the cut scenes. The whole "immigrant looking for a justified revenge" thing in say "Grand Theft Auto IV" is a direct parallel to the storyline of previous games where the protagsnist was say a sociopath looking for his stolen drugs, or simply trying to take over the city "Scarface" style. I also can't help but wonder if the choice of minority protaganists (immigrants, blacks, etc..) is also an attempt to sway criticism by being able to use the old arguement that it isn't racist if the person doing it isn't white... allowing it to use a similar defense as say rap music.
A lot of people won't like what I'm saying, but the bottom line is that if we're going to see zombies get returned to the grave, we also need to bury political correctness.
I'll also say that I don't think I'm anywhere near close to being the only one who has noticed this trend. I think a lot of these "zombies are people too" movies and stories are sort of poking fun at the idea for specifically that reason, making them fairly meta.
In 10 years if things continue I suspect instead of seeing some hold outs with human opponents, human enemies, especially based in the "real world" will be gone entirely. I think the tired old cliques like zombies don't continue because of a fad, but for other reasons and it won't change without bigger changes throughout society... namely killing political correctness, at least in the media, which has to start by getting it's supporters out of positions of control so they can't try and work that agenda through the media.